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    SBF1 SET binding factor 1 [ Homo sapiens (human) ]

    Gene ID: 6305, updated on 7-Jan-2024

    Summary

    Official Symbol
    SBF1provided by HGNC
    Official Full Name
    SET binding factor 1provided by HGNC
    Primary source
    HGNC:HGNC:10542
    See related
    Ensembl:ENSG00000100241 MIM:603560; AllianceGenome:HGNC:10542
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MTMR5; CMT4B3; DENND7A
    Summary
    This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]
    Expression
    Broad expression in testis (RPKM 38.3), brain (RPKM 19.4) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SBF1 in Genome Data Viewer
    Location:
    22q13.33
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50445000..50475035, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50954193..50984219, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50883429..50913464, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 6 regulatory subunit 2 Neighboring gene RNA, 7SL, cytoplasmic 500, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50836255-50836755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50838165-50838761 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:50844619-50845818 Neighboring gene microRNA 12114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50883030-50883876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50910985-50911896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50911897-50912806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50913717-50914626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13982 Neighboring gene adrenomedullin 2 Neighboring gene myo-inositol oxygenase

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC99700, DKFZp761D0422

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in protein dephosphorylation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    myotubularin-related protein 5
    Names
    DENN/MADD domain containing 7A
    inactive phosphatidylinositol 3-phosphatase 5

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_041810.1 RefSeqGene

      Range
      5037..35072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001365819.1NP_001352748.1  myotubularin-related protein 5 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93186.1
      UniProtKB/Swiss-Prot
      A0A024R4Z9, A6PVG9, G5E933, O60228, O95248, Q5JXD8, Q5PPM2, Q96GR9, Q9UGB8
      UniProtKB/TrEMBL
      A0A8I5KXX8
      Related
      ENSP00000510414.1, ENST00000689129.1
      Conserved Domains (7) summary
      smart00801
      Location:365433
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:130311
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:186
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:17611866
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam06602
      Location:11291532
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:544765
      SBF2; Myotubularin protein
      cl17171
      Location:8941012
      PH-like; Pleckstrin homology-like domain
    2. NM_001410794.1NP_001397723.1  myotubularin-related protein 5 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93187.1
      UniProtKB/TrEMBL
      A0A8I5KVF2
      Related
      ENSP00000509117.1, ENST00000684986.1
    3. NM_001410795.1NP_001397724.1  myotubularin-related protein 5 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL096767
      Consensus CDS
      CCDS93185.1
      UniProtKB/TrEMBL
      A0A8I5KXX8, A0A8J8YTQ8
      Related
      ENSP00000252027.8, ENST00000348911.11
    4. NM_002972.4NP_002963.2  myotubularin-related protein 5 isoform 1

      See identical proteins and their annotated locations for NP_002963.2

      Status: REVIEWED

      Source sequence(s)
      AL096767, BC087612, BM975530, HY035781
      Consensus CDS
      CCDS14091.2
      UniProtKB/TrEMBL
      A0A8I5KVF2
      Related
      ENSP00000370196.2, ENST00000380817.8
      Conserved Domains (8) summary
      smart00801
      Location:364432
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:129310
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:186
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:17861891
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam00169
      Location:17901891
      PH; PH domain
      pfam06602
      Location:11281556
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:543764
      SBF2; Myotubularin protein
      cl17171
      Location:8931011
      PH-like; Pleckstrin homology-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      50445000..50475035 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      50954193..50984219 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)